The casualties included a 40-year-old State Emergency Service volunteer, Emergency Services Minister Troy Grant said, reports Efe news.
The volunteer collapsed on duty as he assisted with rescue efforts in Wollongong, south of Sydney.
Another person, a 14-year-old boy, died in a car crash on a flooded road in Thornleigh on upper north shore of the city, police said.
Two police officers were injured when a tree branch fell on a car while they were assisting motorists who were stuck in floodwaters on Pittwater Road in North Ryde.
The Bureau of Meteorology for New South Wales said several places in Sydney had received more than 100mm of rain on what it called the city's "wettest day since 1984".
Several roads, lanes and bylanes were inundated since the morning commute hours, leading to multiple closures, while several rail services were either cancelled or delayed.
Dozens of domestic and international flights were cancelled or delayed as Sydney Airport closed two of its runways amid high-speed winds.
Thousands of homes and offices faced blackouts as power supplies were disrupted for several hours in many areas across New South Wales.
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